Project Summary Periodontitis is thought to have a strong genetic background, but our knowledge on the determinants of susceptibility to this inflammatory disease is still incomplete and hinders the development of effective personalized medicine approaches to its prevention and treatment. Likewise, the molecular underpinnings governing the progression of the disease, from states of periodontal health to gingivitis to severe periodontitis, are still inadequately understood. Emerging evidence suggests an important role of epigenetic regulation in diverse pathologic conditions that have an inflammatory component. This project will adopt a combined genetic/epigenetic strategy to study periodontitis susceptibility and pathogenesis. In our first aim, we will examine if earlier identified genetic loci associated with the extent and severity of periodontitis or with colonization by certain bacterial species can be replicated in the Washington Heights/Inwood Community Aging Project (WHICAP), a community based cohort of elderly individuals with available clinical periodontal data and subgingival microbial profiles assessed through next generation sequencing. We will produce a list of candidate genes and simple nucleotide polymorphisms, including both statistically significant and suggestive GWAS signals, which we will bring forward for cross-validation and fine mapping. In our second aim, we hypothesize that mapping of haplotype-dependent allele-specific DNA methylation (hap-ASM) and methylation quantitative trait loci (mQTLs) in key cell types in the peripheral blood and in the gingival tissues of patients with periodontitis will identify true-positive GWAS signals for periodontitis susceptibility. In a new cohort of periodontitis patients, we will produce genome-wide maps of cell-specific hap-ASM and mQTLs using microarray-based and next generation bisulfite sequencing, and will overlap these maps with the supra- and sub-threshold GWAS peaks from aim 1. Identification of loci that score positively in both types of data will allow us to pinpoint bona fide regulatory haplotypes and specific regulatory sequence elements that mediate inter- individual differences in susceptibility to periodontitis. In our third aim, we will test the hypothesis that mapping of gene-specific DNA methylation patterns in gingival tissue cells from healthy and periodontitis-affected sites will reveal epigenetically regulated genes and pathways relevant to the pathogenesis of periodontitis. In the same patients as in Aim 2, we will assess changes in CpG methylation and hydroxymethylation in laser- capture micro-dissected epithelial cells and fibroblasts from periodontitis-affected vs. healthy gingiva, and will validate our findings using immunohistochemical markers and gene expression assays. We expect that our novel, combined genetic/epigenetic approach will improve our ability to identify periodontitis-susceptible individuals, will enhance our understanding of the tissue-localized responses in periodontitis pathogenesis, and will ultimately inform the design of a personalized medicine approach to periodontitis prevention and treatment. 1